[BioC] metabolomics data analysis

[James W. MacDonald]

On Wednesday, September 04, 2013 10:29:33 AM, guest [guest] wrote:
>
> Dear Users,
>
> Do you know any package is designed for metabolomics data? or any package can be used to analyze metabolomics data? I have no experience analyze metabolomics data, it should be quite different from microarray.

You need to be more clear in what you are asking for. What exactly do 
you mean by metabolomics data? Is this mass spectrometry data? In 
addition, what do you mean by analyze? If MS data, I suppose analyze 
could be peak detection, or it could be statistical analysis of the 
metabolomics data (e.g., testing for differences in metabolite levels).

Best,

Jim


>
> Thanks,
>
>
>   -- output of sessionInfo():
>
>> sessionInfo()
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] splines   parallel  stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>   [1] WGCNA_1.27-1                          doParallel_1.0.3                      iterators_1.0.6                       foreach_1.4.1
>   [5] MASS_7.3-27                           reshape_0.8.4                         plyr_1.8                              Hmisc_3.12-2
>   [9] Formula_1.1-1                         survival_2.37-4                       flashClust_1.01-2                     dynamicTreeCut_1.60
> [13] impute_1.34.0                         affy_1.38.1                           cluster_1.14.4                        preprocessCore_1.22.0
> [17] BiocInstaller_1.10.3                  pd.hugene.2.0.st_3.8.0                oligo_1.24.2                          oligoClasses_1.22.0
> [21] hugene20sttranscriptcluster.db_2.12.1 org.Hs.eg.db_2.9.0                    RSQLite_0.11.4                        DBI_0.2-7
> [25] AnnotationDbi_1.22.6                  Biobase_2.20.1                        BiocGenerics_0.6.0                    limma_3.16.7
>
> loaded via a namespace (and not attached):
>   [1] affxparser_1.32.3    affyio_1.28.0        Biostrings_2.28.0    bit_1.1-10           codetools_0.2-8      ff_2.2-11            GenomicRanges_1.12.5
>   [8] grid_3.0.1           IRanges_1.18.3       lattice_0.20-15      rpart_4.1-1          stats4_3.0.1         tools_3.0.1          zlibbioc_1.6.0
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099